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(v3.0.0.9003) eucast_rules fix, new tidymodels integration

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dr. M.S. (Matthijs) Berends
2025-06-13 14:03:21 +02:00
parent 3742e9e994
commit 72db2b2562
22 changed files with 760 additions and 107 deletions
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28
man/random.Rd
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@ -7,19 +7,25 @@
\alias{random_sir}
\title{Random MIC Values/Disk Zones/SIR Generation}
\usage{
random_mic(size = NULL, mo = NULL, ab = NULL, ...)
random_mic(size = NULL, mo = NULL, ab = NULL, skew = "right",
severity = 1, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, skew = "left",
severity = 1, ...)
random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)
}
\arguments{
\item{size}{Desired size of the returned vector. If used in a \link{data.frame} call or \code{dplyr} verb, will get the current (group) size if left blank.}
\item{mo}{Any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}.}
\item{mo}{Any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be the same length as \code{size}.}
\item{ab}{Any \link{character} that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
\item{skew}{Direction of skew for MIC or disk values, either \code{"right"} or \code{"left"}. A left-skewed distribution has the majority of the data on the right.}
\item{severity}{Skew severity; higher values will increase the skewedness. Default is \code{2}; use \code{0} to prevent skewedness.}
\item{...}{Ignored, only in place to allow future extensions.}
\item{prob_SIR}{A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value).}
@ -31,17 +37,25 @@ class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=a
These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
}
\details{
The base \R function \code{\link[=sample]{sample()}} is used for generating values.
Generated values are based on the EUCAST 2025 guideline as implemented in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the \code{skew} and \code{severity} arguments:
\itemize{
\item \code{skew = "right"} places more emphasis on lower MIC or higher disk values.
\item \code{skew = "left"} places more emphasis on higher MIC or lower disk values.
\item \code{severity} controls the exponential bias applied.
}
}
\examples{
random_mic(25)
random_disk(25)
random_sir(25)
# add more skewedness, make more realistic by setting a bug and/or drug:
disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
plot(disks)
# `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")
\donttest{
# make the random generation more realistic by setting a bug and/or drug:
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4